The overall aim of Project 3 Biopharmaceutics/Drug Design is to iteratively design protease inhibitors with desired specificity (broad-spectrum or specific) and transport properties (systemic or localized distribution), in cooperation with Project I Synthesis and Project 4 in vitro Cellular Interactions. The programmed inhibitor properties determine the dosing route and potential side effects of the inhibitor. For instance, broad-spectrum inhibitors with systemic distribution will be suitable for oral delivery and treatment of organism-wide conditions like metastases. Their side effects, however, can be significant. Specific inhibitors with localized distribution require local administration, either direct (injection, topical application) or systemic in a targeted dosage form. They will treat local conditions like tumor growth and their side effects will be minimized. The design will be based on description of individual steps in the protease inhibition in terms of structure and properties of inhibitors using conceptual quantitative structure-timeactivity relationships (QSTAR). The measured individual steps include distribution of inhibitors in cells and tissue cultures, binding of inhibitors to the extracellular matrix, and toxicity. The measured inhibitor properties are lipophilicity, amphiphilicity (the association constant to a phospholipid/water interface), acidity, solubility, and reactivity. Enzyme kinetics of inhibition for various proteases will be determined and described using (1) 3D-structure-based models where feasible, (2) homology-based models where no 3D-structures are available, and (3) 3D-QSTAR methods that infer the details of an unknown binding site using the binding energies of a set of chemicals. The binding site will be either the active site of a protease for designing specific inhibitors or a superposition of active sites of several proteases for designing broad-spectrum inhibitors. Using a combination of molecular mechanics and quantum mechanics (for description of covalent steps), QSTAR will be constructed for individual rate/equilibrium (micro)constants that characterize the time course of inhibition. Design of inhibitors will be based on the results of in vitro tests performed in Project 4. Conceptual QSTAR for individual steps are transferable between complexity levels (enzymes, cells, in vitro systems) and will facilitate the construction of QSTAR for the in vitro systems.